Assessing the diversity of rhizobia communities associated with legume hosts using a novel multilocus sequencing approach

Project Description

Our project involves the symbiotic relationship of leguminous plants with bacteria that reside within nodules located on the plant’s roots (henceforth referred to as rhizobia). Within nodules, plants provide rhizobia with a source of carbon while rhizobia fix atmospheric nitrogen for the plant. Depending on the availability of other nitrogen sources in the soil (e.g., nitrate, ammonia), the effectiveness of nitrogen fixation exhibited by rhizobia can have a huge impact on the growth and persistence of legume host populations. Recent field surveys attempting to quantify rhizobia diversity have revealed a tremendous amount of variation, both in terms of genetic identity and nitrogen fixation effectiveness when paired with host plants. However, these studies often involve a limited diversity of hosts and use sequencing techniques that likely underestimate rhizobial diversity. By using a novel multilocus sequencing approach, we hope to compare the natural diversity of rhizobia associated with several legume species (native and introduced) that occur around KSR. In doing so, we hope to address several questions, including whether different legume species exhibit varying degrees of selectivity (i.e., only associate with specific strains), or whether hosts tend to pick up the most dominate strain at a given site.  Overall, we hope to add significantly to the growing database on rhizobial biodiversity, and generate hypotheses that we can later test in field studies.

Additional Scientific Information

The overall goal will be to supplement the few studies specifically focusing on the natural diversity of rhizobia and how this might affect the specificity of the host. Specifically, the natural abundance and diversity of rhizobia in the soil will be assessed and compared to strains of rhizobia actually associated with the host. This will involve collecting soil samples and nodules for extraction. Diversity and abundance will be assessed using genetic techniques. The initial plan is to use quantitative PCR in conjunction with high throughput sequencing (eg., Illumina) to assess rhizobial diversity; however, this approach might not be feasible because it is relatively novel and may require lots of time for trial and error, not to mention data analysis. An alternative approach is to use pre-designed sets of primers (eg., Sarita et al 200! 5) that have been used to distinguish rhizobia from other bacteria in the soil and estimate diversity and abundance. By assessing natural rhizobial diversity at several sites at KSR, many follow up experiments can be later conducted to test the hypotheses that might be generated.

Movie of sampling for soil rhizobia associated with legumes

Principal InvestigatorMegan Frederickson
Researcher(s): Rebecca Batstone

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